Showing : scrnaseq • reset
0
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2
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213
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
7 days ago • updated 5 days ago Quang NN ▴ 10
2
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2
replies
486
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 5 months ago by ▴ 10
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0
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435
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
7 months ago Damini • 0
1
vote
8
replies
1.1k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 6 months ago by 52k • written 7 months ago by • 0
0
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0
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347
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
8 months ago Bibi • 0
0
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1
reply
604
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 months ago by ★ 4.6k • written 10 months ago by • 0
0
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2
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695
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
10 months ago rocanja ▴ 60
0
votes
1
reply
485
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
1
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2
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1.5k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
14 months ago ruba-mahmoud • 0
0
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2
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963
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
16 months ago Momo • 0
0
votes
1
reply
623
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 18 months ago by ★ 4.6k • written 18 months ago by • 0
2
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5
replies
1.4k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
18 months ago • updated 17 months ago duez.tolga • 0
0
votes
1
reply
1.9k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 18 months ago by ★ 4.6k • written 18 months ago by • 0
4
votes
3
replies
1.4k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 18 months ago by 52k • written 18 months ago by • 0
0
votes
1
reply
676
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 18 months ago by ★ 4.6k • written 18 months ago by • 0
0
votes
1
reply
758
views
library(topGO) query
topGO scRNAseq
updated 18 months ago by ▴ 780 • written 18 months ago by • 0
0
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0
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598
views
adding noise to scRNA Seq counts
scRNAseq
18 months ago Jiyuan • 0
1
vote
11
replies
7.0k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 15 months ago by • 0 • written 19 months ago by • 0
2
votes
3
replies
1.7k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
20 months ago Lluís Revilla Sancho ▴ 760
0
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0
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778
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
20 months ago info ▴ 10
0
votes
1
reply
835
views
scRNAseq Download Errors
scRNAseq
updated 21 months ago by 4.1k • written 21 months ago by ★ 1.5k
2
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0
replies
1.9k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
22 months ago Tadeoye ▴ 20
0
votes
1
reply
1.2k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 23 months ago by ▴ 750 • written 23 months ago by ▴ 10
4
votes
5
replies
2.1k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 23 months ago by ▴ 750 • written 23 months ago by ▴ 10
0
votes
2
replies
1.1k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 15 months ago by • 0 • written 23 months ago by • 0
0
votes
3
replies
1.7k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 6 months ago by • 0 • written 2.2 years ago by • 0
1
vote
2
replies
1.6k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.3 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.2k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
2.3 years ago evocanres • 0
0
votes
3
replies
1.4k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
2.3 years ago Madiha • 0
4
votes
5
replies
3.4k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
2.5 years ago Peter Hickey ▴ 750
4
votes
2
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1.5k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
2.5 years ago Guandong Shang ▴ 40
0
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4
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2.6k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.5 years ago by ★ 28k • written 2.5 years ago by ▴ 40
0
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0
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1.2k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
2.5 years ago peter.kharchenko ▴ 30
0
votes
0
replies
926
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.5 years ago Sebastian Lewandowski • 0
1
vote
4
replies
1.6k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
2.5 years ago Chise ▴ 10
0
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0
replies
1.3k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.6 years ago Guandong Shang ▴ 40
0
votes
2
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2.4k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 2.6 years ago by ★ 4.6k • written 2.6 years ago by • 0
0
votes
1
reply
1.5k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 2.6 years ago by ★ 4.6k • written 2.6 years ago by • 0
2
votes
8
replies
2.1k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.6 years ago Kelen ▴ 10
0
votes
1
reply
962
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
1
vote
2
replies
2.4k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.8 years ago Ismail • 0
1
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1
reply
2.3k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.8 years ago by ▴ 750 • written 2.8 years ago by • 0
2
votes
2
replies
1.6k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.0 years ago • updated 2.9 years ago behr201 • 0
2
votes
2
replies
1.6k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3.0 years ago Hasan Alanya • 0
0
votes
1
reply
1.3k
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.8 years ago by ▴ 20 • written 3.0 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.0 years ago Sebastian Lewandowski • 0
0
votes
3
replies
1.9k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
3.2 years ago • updated 3.1 years ago zahra.mesri95 • 0
0
votes
0
replies
807
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.2 years ago Núria • 0
0
votes
2
replies
1.2k
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 3.3 years ago by ★ 1.4k • written 3.4 years ago by • 0
2
votes
4
replies
1.6k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
3.5 years ago mbenegas ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Find exact GRanges match keeping metadata columns by Michael Love 43k
You could use `minoverlap` but that requires an integer, not a fraction: ``` gr1 |> join_overlap_left(gr2, minoverlap=6) ``` Plyranges do…
Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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